SMTL ID : 9dl2.2 (2 other biounits)

Structure of proline utilization A complexed with 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 32 residues within 4Å: Chain A: D.308, A.309, V.340, Q.342, Y.344, R.369, V.371, K.372, G.373, A.374, Y.375, W.376, F.394, T.395, R.396, K.397, T.400, A.423, T.424, H.425, N.426, Q.449, C.450, L.451, Y.475, E.494, N.495, S.499, S.500, F.501, I.1234, G.1235 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:A.423, A:Q.449, A:Y.475 Hydrogen bonds: A:A.309, A:A.309, A:Q.342, A:R.369, A:K.372, A:G.373, A:G.373, A:G.373, A:A.374, A:T.395, A:K.397, A:T.400, A:D.401, A:T.424, A:H.425, A:H.425, A:N.426, A:N.426, A:E.494, A:S.499, A:F.501 Water bridges: A:K.267, A:Y.475, A:Y.475, A:V.502 Salt bridges: A:K.372, A:K.372, A:K.397 pi-Stacking: A:W.376, A:W.376

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: L.1080, G.1081, L.1098, H.1099 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1081 Water bridges: A:A.1100 PEG.5: 4 residues within 4Å: Chain A: Y.239, P.289, R.290, A.293 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.290, A:R.290, A:R.290 PEG.7: 6 residues within 4Å: Chain A: A.572, M.574, K.575, V.603, V.604, G.605 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.575, A:R.661 Water bridges: A:D.602, A:D.602, A:D.602, A:V.603, A:S.606

1 x 53E: 2,3-dihydro-1,4-benzodioxine-5-carboxylic acid(Non-covalent)

53E.3: 10 residues within 4Å: Chain A: E.673, E.676, F.710, A.713, R.845, S.847, I.1003, G.1004, A.1005, F.1012 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.845, A:S.847, A:G.1004, A:A.1005 Water bridges: A:R.845 Salt bridges: A:R.845 pi-Stacking: A:F.710, A:F.1012

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: R.42, L.388, A.389, D.554 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.389 Water bridges: A:R.42, A:D.554, A:N.557, A:T.560 FMT.6: 2 residues within 4Å: Chain A: S.31, T.32 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.32, A:T.32 Water bridges: A:S.31, A:S.31, A:L.33

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.8: 30 residues within 4Å: Chain A: I.705, S.706, P.707, W.708, N.709, F.710, I.714, K.732, P.733, A.734, E.735, D.764, G.765, G.768, A.769, F.782, T.783, G.784, S.785, V.788, I.792, E.812, T.813, G.814, C.846, E.942, F.944, L.972, F.1012 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.707, A:F.710, A:I.714, A:T.783 Hydrogen bonds: A:S.706, A:S.706, A:W.708, A:K.732, A:E.735, A:S.785, A:T.813, A:E.942 Water bridges: A:W.708, A:E.736, A:T.786

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 3 residues within 4Å: Chain A: R.690, P.1041, Q.1042 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.1042 Water bridges: A:R.690, A:R.690 Salt bridges: A:R.690 SO4.10: 6 residues within 4Å: Chain A: S.139, Q.855, E.856, D.857, R.954, R.955 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.855, A:D.857, A:R.955 Water bridges: A:D.956 Salt bridges: A:R.954 SO4.11: 3 residues within 4Å: Chain A: K.1062, A.1138, K.1141 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1062 SO4.12: 4 residues within 4Å: Chain A: S.1196, G.1198, E.1199, R.1202 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.1196, A:S.1196, A:G.1198, A:E.1199 Water bridges: A:R.1202, A:R.1202 Salt bridges: A:R.1202 SO4.13: 4 residues within 4Å: Chain A: R.71, S.511, I.512, D.513 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.512, A:D.513 Salt bridges: A:R.71

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.14: 1 residues within 4Å: Ligands: NAD.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meeks, K.R. et al., Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-gamma-semialdehyde Dehydrogenase. Molecules (2024)

Release Date

2024-11-27

Peptides

Bifunctional protein PutA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional protein PutA

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